Gastro-Intestinal Biomarkers for Diagnosis and Therapies of Proteinopathies

Abstract

Pharmaceutical composition for the treatment of proteinopathies comprising products which are able to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

Claims

1. A pharmaceutical composition for the treatment of proteinopathies comprising products that stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in a gut of an individual.

2. The pharmaceutical composition according to claim 1 wherein the products are bacteria-generated products including at least one of proteins, carbohydrates, nucleic acids, lipids, and short chain fatty acids.

3. The pharmaceutical composition according to claim 1 for the treatment of Alzheimer's Disease.

4. A method for determining an appropriate treatment of proteinopathies using a composition including products that stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in a gut of an individual, the method comprising a step of: determining a relative abundance of the at least one of Odoribacter, Oscillospira, Dehalobacterium, Ali stipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population that is below or above a predetermined abundance or predetermined baseline.

5. The method according to claim 4 further comprising a step of: preparing a composition including products to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population, to reach the baseline.

Description

DETAILED DESCRIPTION OF THE INVENTION

[0020] Referring to FIG. 1 an individual is diagnosed for his cognitive impairments induced by a proteinopathy (35) and/or by measuring its microbiota spectrum (31).

[0021] This microbiota spectrum (31) of a human individual contains at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population. The genomic DNA of microbiota is extracted from the feces i.e. the waste product originating from the gut of the individual. This microbiota spectrum (31) is assessed using profiling methods including screening of 16SrRNA genes by PCR and high-throughput methods such as pyrosequencing, allowing the identification of bacterial genes that are differentially represented in an individual. This allows determining a relative abundance of the at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population that is below or above a predetermined abundance or predetermined baseline.

[0022] Based on these findings an appropriate therapeutic decision is taken (50), which aims at a modulation of the of at least Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population by administrating probiotics (21), prebiotics (22), purified prebiotics (23) and/or antibiotics (24) as an isolated intake or a mixture or a combination of administrated means (20; comprising 21-24) or any mean to alter the microbiota spectrum for aiming a positive therapeutic result. This therapy (100) can be a single administration or consist in a repetitive administration until a positive therapeutic effect is achieved.

[0023] This invention describes in at least one aspect, a protein assay that includes protein extracted from the microbiota of a human individual to an assay that determines at least one protein indicative of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population.

[0024] Products produced by Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria including but not limited to proteins, carbohydrates, nucleic acids and/or lipids or more specifically short chain fatty acids, are used for modifying the microbiota in the gastrointestinal tract of an individual as part of a therapeutic regimen for treating AD.

[0025] In at least one aspect, a method of treating a human individual with proteinopathies, includes administering to the individual, bacteria-generated products including proteins, carbohydrates, nucleic acids and/or lipids or more specifically short chain fatty acids, to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

[0026] In at least one aspect, a method of treating a human individual with AD, includes administering to the individual, bacteria-generated products including proteins, carbohydrates, nucleic acids and/or lipids or more specifically short chain fatty acids, to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

[0027] This invention describes, a method of treating a human individual with proteinopathies, including the administration to the individual, prebiotics (proteins, carbohydrates, nucleic acids and/or lipids or more specifically short chain fatty acids), to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

[0028] In at least one aspect, a method of treating a human individual with AD, includes administering to the individual, prebiotics (proteins, carbohydrates, nucleic acids and/or lipids or more specifically short chain fatty acids), to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

[0029] This invention describes, a method of treating a human individual with proteinopathies, including the administration to the individual, probiotics including Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

[0030] This invention describes, a method of treating a human individual with AD including the administration to the individual, probiotics including Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

[0031] This invention describes, a method of treating a human individual with proteinopathies, including the administration to the individual of pharmaceutical compound to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

[0032] This invention describes, a method of treating a human individual with AD, including the administration to the individual of pharmaceutical compound to stimulate growth or inhibition of at least one of Odoribacter, Oscillospira, Dehalobacterium, Alistipes, Parabacteroides, Lactobacillus and Sutterella, Firmicutes, Bacteroidetes, Allobaculum and Akkermansia bacteria population in the gut of individuals.

DETAILED DESCRIPTION OF FIGURES

[0033] Referring to FIG. 1 as the shows the cerebral and plasmatic soluble Aβ and the reduction of cerebral and plasmatic soluble Aβ levels in GF-APPPS1 transgenic mice. Levels of cerebral soluble Aβ38 (a), Aβ40 (b), Aβ42 (c) and ratio Aβ42/Aβ40 (d) as measured by ELISA in 3.5 (n=7) and 8 (n=7) month-old conventionally-raised (CONVR-APPPS1) and in comparison to germ free (GF-APPPS1) APPPS1 mice. Levels of Aβ are assessed by western blot in 3.5 month-old (n=5) (e) and in 8 month-old mice (n=6) (f). The relative densities in (e) are shown aside and indicate the relative density of (Aβ/tubulin) and (APP/tubulin) for CONV-APPPS1 in comparison to GF-APPPS1 mice. This teaching is equivalent in (f) but for 8-month old mice for both mice species. Plasmatic levels of soluble Aβ40 (g), Aβ42 (h) and ratio Aβ42/Aβ40 (i) measured by ELISA.

[0034] Referring to FIG. 2 an individual is diagnosed for his cognitive impairments induced by a proteinopathy (35) and/or by measuring its microbiota spectrum (31). An appropriate therapeutic decision is taken (50), which aims at modulating gut microbiota by administrating probiotics (21), prebiotics (22), purified prebiotics (23) and/or antibiotics (24) as an isolated intake or a mixture or a combination of administrated means (20; comprising 21-24). This therapy (100) can be a single administration or consist in a repetitive administration until a positive therapeutic effect is achieved.

[0035] Referring to FIG. 3A to FIG. 3C are Cladograms generated with LDA Effect Size (LEfSE) analysis for 219,712 randomly selected sequences/sample illustrating enrichment of the phylum Bacteroidetes in APPPS21 (CONV) mice while WT mice show enriched in Firmicutes and Verrucomicrobia. The size of circles is proportionate to each taxon's mean relative abundance. At genus level, unclassified genera of S24-7 and Rikenellaceae were increased in APPPS21 mice, and Allobaculum and Akkermansia in WT mice. FIG. 3A-C shows cladograms, where FIG. 3A shows the relative abundance of gut-bacteria in conventially raised APPPS1 mice, FIG. 3B in WT mice and FIG. 3C the overlay for both mice in a full cladogram. FIG. 3D is the associated table for naming the bacteria. The tables in FIG. 3A name the bacteria for cladogram shown in FIG. 3A, similar teaching is valid for FIG. 3B.

[0036] Referring to FIG. 4 as mean sequence relative abundance of gut microbiota in 8-months-old transgenic APPPS21 (n=7) and wild type (WT, n=6)) mice, at phylum (top left) and genus (middle left) level. LEfSE analysis revealed 8 differentially abundant phyla (bottom left) and 28 genera (right) (α=0.01) with an LDA score higher than 2 when comparing transgenic APPPS21 and WT mice.

[0037] Referring to FIG. 5 as an orthogonal partial least squares (OPLS) scatter plot of correlations between different gut microbial genera (x-variables) and cerebral soluble Aβ42 (Brain Aβ42; y-variable) in 8 months old conventional transgenic APPPS21 mice.

Definitions Terms and Elements

[0038] Amyloid: Amyloids are insoluble fibrillar protein aggregates that share specific structural traits. Amyloids arise from at least 20 misfolded proteins and polypeptides present naturally in the body. These inappropriately folded structures alter their proper configuration such that they erroneously interact with one another or other cell components forming insoluble fibrils. Amyloids have been associated with the pathology of more than 20 serious human diseases in that, abnormal accumulation of amyloid fibrils in organs may lead to amyloidosis, and may play a role in various neurodegenerative disorders

[0039] Proteinaceous: Of, relating to, consisting of, resembling, or pertaining to protein, or pertaining to any material having a protein base.

[0040] Proteinopathy: Proteinopathy refers in medicine to a class of diseases in which certain proteins become structurally abnormal, and thereby disrupt the function of cells, tissues and organs of the body. Frequently the proteins fail to fold into their normal configuration; in this misfolded state, the proteins can become toxic in some way (a gain of toxic function) or they can lose their normal function. The proteinopathies (also known as proteinopathies, protein conformational disorders, or protein misfolding diseases) include diseases such as prion diseases, Alzheimer's disease, Parkinson's disease, type 2-diabetes, and a wide range of other central and peripheral disorders. The concept of proteopathy can trace its origins to the mid-19th century, when, in 1854, Rudolf Virchow coined the term amyloid (“starch-like”) to describe a substance in cerebral corpora amylacea that exhibited a chemical reaction resembling that of cellulose. In 1859, Friedreich and Kebulé demonstrated that, rather than consisting of cellulose, “amyloid” actually is rich in protein. Subsequent research has shown that many different proteins can form amyloid, and that all amyloids have in common birefringence in cross-polarized light after staining with the dye Congo Red, as well as a fibrillar ultrastructure when viewed with an electron microscope.

[0041] Proteolysis: Proteolysis is the directed degradation or digestion, of proteins by cellular enzymes called proteases or by intra-molecular digestion.

[0042] Seeded proteinopathies: Some proteins can be induced to form abnormal assemblies by exposure to the same or similar protein assembly that has folded into a disease-causing conformation, a process called ‘seeding’ or ‘permissive templating’. In this way, the disease state can be brought about in a susceptible host by the introduction of diseased tissue extract from an afflicted donor. The most known form of such inducible proteopathy is prion disease (e.g., Creutzfeldt Jakob), which can be transmitted by exposure of a host organism to purified prion protein in a disease-causing conformation. There is now evidence that other proteinopathies can be induced by a similar mechanism, including but not restricted to A13 amyloidosis, tauopathy and synucleinopathy. In all of these instances, an aberrant form of the protein itself appears to be the pathogenic agent. In some cases, the deposition of one type of protein can be experimentally induced by aggregated assemblies of other proteins that are rich in β-sheet structure, possibly because of structural complementarity of the protein molecules. There is also experimental evidence for cross-seeding between prion protein and Aβ or between tau and Aβ.

[0043] Microbiota/Microflora: The term “microbiota or microflora” refers to the whole microbial community found in the gastro-intestinal tract of a higher organism, including bacteria, archaea, yeasts, and various parasites.

[0044] Microflora modulation: Refers to a change in the representation of bacteria in a microbiological community of a particular individual.Microflora can be modulated bycompounds that induce the growth and/or activity of commensal microorganisms that contribute to the well-being of their host. These molecules called prebiotics are present in diet or in the gastro-intestinal tract and are typically but not exclusively non-digestible fibers compounds that stimulate the growth and/or activity of beneficial bacteria that colonize the large bowel by acting as substrate for them. Microflora can also be modulated by microorganisms. These live micro-organisms called probiotics, when administered adequately, confer a health benefit to the host. Gastro-intestinal microflora can be also modulated by antibiotics. These molecules refer to any substance produced by a living microorganism which is antagonistic to the growth and/or division of other living microorganisms. Nutritional approach leading to modulation of gut microbiota by a combination of probiotics and prebiotics are commonly referred as synbiotics. These molecules include carbohydrates, proteins, nucleic add and lipids.

[0045] Short chain fatty acids: are lipids which constitute a sub-group of fatty acids. They includes Acetic acid, Propionic acid, Isobutyric acid (2-methylpropanoic acid), Butyric acid, Isovaleric acid (3-methylbutanoic acid) and Valeric acid (pentanoic acid).

[0046] Features that allow specific modulation of microflora: Specifications that differentiate a defined microbial community from the rest of the microbes that may coexist in the same GI tract. These features include the identification and administration of any microbial-generated molecules associated with the aforementioned distinct microbial community. These molecules may be, but not exclusively proteins, carbohydrates, nucleic acids and/or lipids or more specifically short chain fatty acids.

[0047] Microbiome analysis: Techniques for characterizing the microbiome include use of nucleic acid and/or proteins. Nucleic acid analysis includes analysis of, DNA, RNA, mRNA, rRNA, and/or tRNA, and can be accomplished using, but not limited to pyrosequencing, qPCR, RT-qPCR, clone libraries, DGGE, T-RFLP, ARISA, micro arrays, FIFH, dot-blot hybridization, next generation sequencing, DNA mapping devices and any other DNA hybridization methods that will detect a specific sequence.

[0048] Proteome analysis: Protein analysis can be performed by 2-Dimensional Gel Electrophoresis, 2-Diminsional Difference Gel Electrophoresis (2D-DIGE), MALDI TOFMS, (2D-) LC-ESI-MS/MS, AQUA, and iTRAQ.

[0049] These characterizations are combined with statistical analysis (Linear discriminant analysis effect size (LEfSE, www.huttenhower.sph.harvard.edu/galaxy/)) to precisely determine the players within the microbiome. Rigorous bioinformatics analysis provides accurate characteristics and distributions of intestinal microflora between individuals. Changes in algorithms or data analysis are known and will in no case represent a novelty for the disclosed claims.